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1.
A genome-wide survey on basic helix-loop-helix transcription factors in rat and mouse 总被引:1,自引:0,他引:1
The basic helix-loop-helix (bHLH) proteins play essential roles in a wide range of developmental processes in higher organisms.
bHLH family members have been identified in over 20 organisms, including nematode, fruit fly, and human. Our study identified
114 rat and 14 additional mouse bHLH members in rat and mouse genomes, respectively. Phylogenetic analyses revealed that both
rat and mouse had 49, 26, 15, 4, 12, and 4 bHLH members in groups A, B, C, D, E, and F, respectively. Only the rat Mxi1 gene has two copies in the genome. All other rat bHLH genes and all mouse bHLH genes are single-copy genes. The chromosomal distribution pattern of mouse, rat, and human bHLH genes suggests the emergence of some bHLH genes through gene duplication, which probably happened at least before the divergence of vertebrates from invertebrates.
The present study provides useful information for future studies using rat as a model animal for mammalian development.
X. Zheng and Y. Wang are jointly first authors.
An erratum to this article can be found at 相似文献
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Plant acyl-CoA dependent acyltransferases constitute a large specific protein superfamily, named BAHD. Using the conserved
sequence motifs of BAHD members, we searched the genome sequences of Populus and Arabidopsis, and identified, respectively, 94- and 61-putative genes. Subsequently, we analyzed the phylogeny, gene structure, and chromosomal
distribution of BAHD members of both species; then, we profiled expression patterns of BAHD genes by “in silico” northern- and microarray-analyses based on public databases, and by RT-PCR. While our genomic- and bioinformatic- analyses
provided full sets of BAHD superfamily genes, and cleaned up a few existing annotation errors, importantly it led to our recognizing
several unique Arabidopsis BAHD genes that inversely overlapped with their neighboring genes on the genome, and disclosing a potential natural anti-sense
regulation for gene expressions. Systemic gene-expression profiling of BAHD members revealed distinct tissue-specific/preferential
expression patterns, indicating their diverse biological functions. Our study affords a strong knowledge base for understanding
BAHD members’ evolutionary relationships and gene functions implicated in plant growth, development and metabolism.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
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Megan E. Andriankaja Selahattin Danisman Lorin F. Mignolet-Spruyt Hannes Claeys Irina Kochanke Mattias Vermeersch Liesbeth De Milde Stefanie De Bodt Veronique Storme Aleksandra Skirycz Felix Maurer Petra Bauer Per Mühlenbock Frank Van Breusegem Gerco C. Angenent Richard G. H. Immink Dirk Inzé 《Plant molecular biology》2014,85(3):233-245
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The DYT1‐interacting proteins bHLH010, bHLH089 and bHLH091 are redundantly required for Arabidopsis anther development and transcriptome 下载免费PDF全文
Engao Zhu Chenjiang You Shuangshuang Wang Jie Cui Baixiao Niu Yingxiang Wang Ji Qi Hong Ma Fang Chang 《The Plant journal : for cell and molecular biology》2015,83(6):976-990
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The MYB Transcription Factor Superfamily of Arabidopsis: Expression Analysis and Phylogenetic Comparison with the Rice MYB Family 总被引:15,自引:0,他引:15
Yanhui C Xiaoyuan Y Kun H Meihua L Jigang L Zhaofeng G Zhiqiang L Yunfei Z Xiaoxiao W Xiaoming Q Yunping S Li Z Xiaohui D Jingchu L Xing-Wang D Zhangliang C Hongya G Li-Jia Q 《Plant molecular biology》2006,60(1):107-124
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Gare Hoon Yeo Felicia S. H. Cheah Christoph Winkler Ethylin Wang Jabs Byrappa Venkatesh Samuel S. Chong 《Development genes and evolution》2009,219(6):289-300
Four members of the twist gene family (twist1a, 1b, 2, and 3) are found in the zebrafish, and they are thought to have arisen through three rounds of gene duplication, two of which occurred
prior to the tetrapod-fish split. Phylogenetic analysis groups most of the vertebrate Twist1 peptides into clade I, except
for the Twist1b proteins of the acanthopterygian fish (medaka, pufferfish, stickleback), which clustered within clade III.
Paralogies and orthologies among the zebrafish, medaka, and human twist genes were determined using comparative synteny analysis of the chromosomal regions flanking these genes. Comparative nucleotide
substitution analyses also revealed a faster rate of nucleotide mutation/substitution in the acanthopterygian twist1b compared to the zebrafish twist1b, thus accounting for their anomalous phylogenetic clustering. We also observed minimal expression overlap among the four
twist genes, suggesting that despite their significant peptide similarity, their regulatory controls have diverged considerably,
with minimal functional redundancy between them.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
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The giant panda (Ailuropoda melanoleuca) is a critically endangered mammalian species. Studies on functions of regulatory proteins involved in developmental processes would facilitate understanding of specific behavior in giant panda. The basic helix-loop-helix (bHLH) proteins play essential roles in a wide range of developmental processes in higher organisms. bHLH family members have been identified in over 20 organisms, including fruit fly, zebrafish, mouse and human. Our present study identified 107 bHLH family members being encoded in giant panda genome. Phylogenetic analyses revealed that they belong to 44 bHLH families with 46, 25, 15, 4, 11 and 3 members in group A, B, C, D, E and F, respectively, while the remaining 3 members were assigned into "orphan". Compared to mouse, the giant panda does not encode seven bHLH proteins namely Beta3a, Mesp2, Sclerax, S-Myc, Hes5 (or Hes6), EBF4 and Orphan 1. These results provide useful background information for future studies on structure and function of bHLH proteins in the regulation of giant panda development. 相似文献
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Tubby-like protein family has been identified in various multicellular organisms, indicating its fundamental functions in
the organisms. However, the roles of plant tubby-like proteins are unknown. In this study, we have defined the tubby-like
protein gene (OsTLP) family with 14 members in rice. Most of the OsTLPs harbor a tubby domain in their carboxyl terminus and an F-box domain
in the amino terminus. The expression of all the OsTLPs was induced on infection of Xanthomonas oryzae pv. oryzae, which causes bacterial blight, one of the most devastating diseases of rice worldwide. The maximal expression levels were
observed at 2–8 h after infection for all the genes. Eight of the 14 OsTLPs were also responsive to wounding. All the OsTLPs showed differential expression in different tissues at different developmental stages. However, four pairs of the 14 OsTLPs, with each pair having high sequence similarity and distributing on the similar position of different chromosomes, showed
similar expression pattern in different tissues, indicating their direct relationship in evolution. These results suggest
that the OsTLP family is involved in host–pathogen interaction and it may be also associated with other physiological and developmental
activities.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
16.
Proteins encoded by the Wnt family of genes act as signals and have been shown to play important roles in a wide variety of developmental processes. Here
we describe the cloning of three Wnt family members from the zebrafish, Danio rerio, which encode proteins with homology to murine Wnt-2, -4 and -5A/B. The expression patterns of the latter two zebrafish genes, designated ZfWnt4 and ZfWnt5 show considerable similarity with their homologues in other vertebrates; ZfWnt2, however, is expressed in the developing viscera in a pattern distinct from its closest murine homologue. In the light of
the similarities and differences in the patterns of expression of these genes relative to their homologues in other vertebrates,
we speculate on their possible functions.
Received 24 October 1995 / Accepted in revised form: 16 January 1996 相似文献
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Ivana Zucchetti Rosaria De Santis Simona Grusea Pierre Pontarotti Louis Du Pasquier 《Immunogenetics》2009,61(6):463-481
Two selected receptor genes of the immunoglobulin superfamily (IgSF), one CTX/JAM family member, and one poliovirus receptor-like
nectin that have features of adhesion molecules can be expressed by Ciona hemocytes, the effectors of immunity. They can also be expressed in the nervous system (CTX/JAM) and in the ovary (nectin).
The genes encoding these receptors are located among one set of genes, spread over Ciona chromosomes 4 and 10, and containing other IgSF members homologous to those encoded by genes present in a tetrad of human
(1, 3 + X, 11, 21 + 19q) or bird chromosomes (1, 4, 24, 31) that include the leukocyte receptor complex. It is proposed that
this tetrad is due to the two rounds of duplication that affected a single prevertebrate ancestral region containing a primordial
leukocyte receptor complex involved in immunity and other developmental regulatory functions.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.
相似文献
Rosaria De Santis (Corresponding author)Email: |
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Cyanophages are ecologically abundant, genetically diverse in aquatic environments, and affect the population and evolutionary
trajectories of their hosts. After reporting the cyanophage Pf-WMP4 genome (Liu et al. in Virology 366:28–39, 2007), we hereby present a related cyanophage, Pf-WMP3, which also infects the freshwater cyanobacterium Phormidium foveolarum. The Pf-WMP3 genome contains 43,249 bp with 234 bp direct terminal repeats. The overall genome organization and core genes
of the two phages are comparable to those of the T7 supergroup phages. Compared with Pf-WMP4, cyanophage Pf-WMP3 has diverged
extensively at the DNA level; however, they are closely related at the protein level and genome architecture. The left arm
genes for the two phages, which mainly encode the DNA replication machinery, are not conserved in the gene order. Whereas
the right arm genes of the two phages coding for structural proteins show high similarity in amino acid sequences and modular
architecture, indicating that they have retained similar development strategies. The differences in similarity levels between
the left and right arm genes suggest that the structural genes are the most conserved elements for a phage.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
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Gyanendra P. Dubey Azeet Narayan Abid R. Mattoo Gajendra P. Singh Raj K. Kurupati Mohd. S. Zaman Anita Aggarwal Renu B. Baweja Sharmila Basu-Modak Yogendra Singh 《Archives of microbiology》2009,191(3):241-253
The propensity of bacterium to sporulate or retain the vegetative form depends on the amount of phosphorylated Spo0A (Spo0A-P), regulated by Spo0E multigene family of phosphatases (Spo0E, YisI and YnzD). Phylogenetic analysis revealed that Spo0E multigene
family of phosphatases (SMFP) descends in two distinct clades of aerobic (Bacillus cluster) and anaerobic (Clostridia cluster) sporulating bacteria. High sequence conservation within species gives a notion
that these members could have evolved through lineage and species-specific duplication event. Of the five genes in Bacillus cereus group, three are pathogen specific, and their synteny suggests that these paralogs could be involved in the regulation of
amino acid metabolism and its transport. Overexpression of B. subtilis Spo0E, an ortholog of SMFP members in B. anthracis (BAS1251), resulted in sporulation deficient phenotype in B. anthracis. B. anthracis Spo0A-P binds to a consensus DNA sequence 5′-TGNCGAA-3′ (‘0A-like box’) and loses its DNA binding ability following treatment with
B. subtilis Spo0E. Thus, B. subtilis Spo0E acts on B. anthracis Spo0A-P and, therefore could complement the function of BAS1251. Further, since ‘0A-like box’ are present in the promoter region
of abrB gene, a known regulator of anthrax toxin gene expression, cross talk among SMFP members and Spo0A-P–AbrB could regulate the expression of anthrax toxin genes.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献